diff --git a/docs/reference/config.md b/docs/reference/config.md
index 6f262d0..b625714 100644
--- a/docs/reference/config.md
+++ b/docs/reference/config.md
@@ -90,7 +90,9 @@ telemetry:
 `transport` is `stdio` or `http` in gateway config files. Legacy
 `streamable-http` and `streamable_http` values are still accepted as aliases
 for `http`.
-The `workspace_root` default controls where sandboxed scripts run. If that
+The `workspace_root` default controls where sandboxed scripts run. When omitted,
+a gateway using the `stdio` transport defaults it to the gateway process's
+current working directory. Other transports use a temporary workspace. If the
 workspace contains `.venv/bin/python` or `.venv/Scripts/python.exe`, the gateway
 uses it for sandbox execution.
 
diff --git a/src/nomad/gateway/sandbox.py b/src/nomad/gateway/sandbox.py
index 448f20a..acdd990 100644
--- a/src/nomad/gateway/sandbox.py
+++ b/src/nomad/gateway/sandbox.py
@@ -466,6 +466,14 @@ async def run_script(
         script_args: list[str] = (),
         capture_stdio: bool = True,
     ) -> SandboxResult:
+        script_path = Path(script_path).expanduser()
+        if not script_path.is_absolute():
+            script_path = (options.workspace_root or Path.cwd()) / script_path
+
+        script_path = script_path.absolute()
+        if not script_path.is_file():
+            raise FileNotFoundError(f"Script file not found: {script_path}")
+
         return await self._run_script_path(
             script_path=script_path,
             options=options,
diff --git a/src/nomad/gateway/server.py b/src/nomad/gateway/server.py
index d87ffe3..9652748 100644
--- a/src/nomad/gateway/server.py
+++ b/src/nomad/gateway/server.py
@@ -421,6 +421,13 @@ def run_gateway(
     **kwargs: Any,
 ) -> None:
     """Run a code-mode gateway from an already-loaded config."""
+    effective_transport = transport or "stdio"
+    if (
+        effective_transport == "stdio"
+        and "workspace_root" not in config.defaults.model_fields_set
+    ):
+        config.defaults.workspace_root = Path.cwd().resolve()
+
     configure_otel(
         service_name=config.telemetry.service_name,
         service_version=_PACKAGE_VERSION,
diff --git a/test/gateway/test_cli.py b/test/gateway/test_cli.py
index 14de15c..064095a 100644
--- a/test/gateway/test_cli.py
+++ b/test/gateway/test_cli.py
@@ -11,12 +11,71 @@
 
 from nomad.common.config_errors import ConfigError
 from nomad.common.upstream_errors import UpstreamConnectionError
-from nomad.gateway import cli
-from nomad.gateway.config import GatewayConfig
+from nomad.gateway import cli, server
+from nomad.gateway.config import GatewayConfig, GatewayDefaults
 
 runner = CliRunner()
 
 
+class _FakeCodeModeGateway:
+    created_with: GatewayConfig | None = None
+
+    def __init__(self, config: GatewayConfig):
+        type(self).created_with = config
+
+    async def serve(self, transport=None, **kwargs):
+        return None
+
+
+@pytest.mark.parametrize("transport", [None, "stdio"])
+def test_stdio_defaults_workspace_to_cwd(
+    monkeypatch,
+    tmp_path: Path,
+    transport: str | None,
+):
+    monkeypatch.chdir(tmp_path)
+    monkeypatch.setattr(server, "CodeModeGateway", _FakeCodeModeGateway)
+    config = GatewayConfig(servers={})
+
+    server.run_gateway(config, transport=transport)
+
+    created = _FakeCodeModeGateway.created_with
+    assert created is not None
+    assert created.defaults.workspace_root == tmp_path.resolve()
+
+
+def test_stdio_preserves_configured_workspace(monkeypatch, tmp_path: Path):
+    launch_dir = tmp_path / "launch"
+    launch_dir.mkdir()
+    configured_workspace = tmp_path / "configured"
+    monkeypatch.chdir(launch_dir)
+    monkeypatch.setattr(server, "CodeModeGateway", _FakeCodeModeGateway)
+    config = GatewayConfig(
+        servers={},
+        defaults=GatewayDefaults(workspace_root=configured_workspace),
+    )
+
+    server.run_gateway(config, transport="stdio")
+
+    created = _FakeCodeModeGateway.created_with
+    assert created is not None
+    assert created.defaults.workspace_root == configured_workspace
+
+
+def test_http_keeps_temporary_workspace_default(monkeypatch, tmp_path: Path):
+    monkeypatch.chdir(tmp_path)
+    monkeypatch.setattr(server, "CodeModeGateway", _FakeCodeModeGateway)
+    config = GatewayConfig(servers={})
+    temporary_workspace = config.defaults.workspace_root
+
+    server.run_gateway(config, transport="http")
+
+    created = _FakeCodeModeGateway.created_with
+    assert created is not None
+    assert created.defaults.workspace_root == temporary_workspace
+    assert created.defaults.workspace_root != tmp_path.resolve()
+
+
 @pytest.fixture
 def dummy_config(tmp_path: Path) -> Path:
     path = tmp_path / "config.yaml"
diff --git a/test/gateway/test_gateway.py b/test/gateway/test_gateway.py
index a30f140..7de534c 100644
--- a/test/gateway/test_gateway.py
+++ b/test/gateway/test_gateway.py
@@ -585,6 +585,81 @@ async def test_execute_script_reads_and_runs_file(
     assert "tool_calls" not in data
 
 
+@pytest.mark.asyncio
+async def test_run_script_resolves_relative_path_from_workspace(
+    gateway: GatewayHarness,
+):
+    workspace_root = gateway.gateway.config.defaults.workspace_root
+    assert workspace_root is not None
+    script_path = workspace_root / "relative.py"
+    script_path.write_text("RESULT = __file__\n", encoding="utf-8")
+
+    result = await gateway.gateway.run_script(Path("relative.py"))
+
+    assert Path(result.result).absolute() == script_path.absolute()
+
+
+@pytest.mark.asyncio
+async def test_run_script_expands_user_path(
+    gateway: GatewayHarness,
+    tmp_path: Path,
+    monkeypatch: pytest.MonkeyPatch,
+):
+    script_path = tmp_path / "home_script.py"
+    script_path.write_text("RESULT = __file__\n", encoding="utf-8")
+    monkeypatch.setenv("HOME", str(tmp_path))
+    monkeypatch.setenv("USERPROFILE", str(tmp_path))
+
+    result = await gateway.gateway.run_script(Path("~/home_script.py"))
+
+    assert Path(result.result).absolute() == script_path.absolute()
+
+
+@pytest.mark.asyncio
+async def test_run_script_resolves_relative_path_from_cwd_without_workspace(
+    gateway: GatewayHarness,
+    tmp_path: Path,
+    monkeypatch: pytest.MonkeyPatch,
+):
+    script_path = tmp_path / "relative.py"
+    script_path.write_text("RESULT = __file__\n", encoding="utf-8")
+    monkeypatch.chdir(tmp_path)
+    gateway.gateway.config.defaults.workspace_root = None
+
+    result = await gateway.gateway.run_script(Path("relative.py"))
+
+    assert Path(result.result).absolute() == script_path.absolute()
+
+
+@pytest.mark.asyncio
+@pytest.mark.parametrize("invalid_name", ["missing.py", "directory"])
+async def test_run_script_rejects_paths_that_are_not_files(
+    gateway: GatewayHarness,
+    invalid_name: str,
+):
+    workspace_root = gateway.gateway.config.defaults.workspace_root
+    assert workspace_root is not None
+    (workspace_root / "directory").mkdir(exist_ok=True)
+
+    with pytest.raises(FileNotFoundError, match="Script file not found"):
+        await gateway.gateway.run_script(Path(invalid_name))
+
+
+@pytest.mark.asyncio
+async def test_execute_script_reports_missing_file_to_client(
+    gateway: GatewayHarness,
+):
+    payload = await gateway.client.call_tool(
+        "execute_mcp_script",
+        {"script_path": "missing.py"},
+        raise_on_error=False,
+    )
+
+    assert payload.is_error
+    assert payload.content
+    assert "Script file not found" in payload.content[0].text
+
+
 @pytest.mark.asyncio
 async def test_execute_script_preserves_file_context_for_package_scripts(
     gateway: GatewayHarness, tmp_path: Path